Determination of inter- and intragenotype stability and variability are the basic tools for the molecular epidemiology and evolutionary investigation of measles virus (MV). We made a comparison between complete genome sequences of four MVs (two wt MV strains-WA.USA/17.98 and 97-45881, and two SSPE MV strains-MVs/Zagreb.CRO/47.02/and MVs/Zagreb.CRO/08.03/), all belonging to genotype D6. Results of analyses clearly confirm that MV genome continuously changes within the viruses of the same or different genotypes by accumulation of mutations in different parts of the genome. Only a small number of these accumulated mutations induce amino acid substitutions and thus possibly introduce new biological characteristics or a new genotype over a long time period. This study clearly reveals a long untranslated region between M and F genes as the most variable region of the MV genome and detects the presence of unique residues on the level of the entire genome as a new important parameter in the investigation of molecular evolution of MVs.
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